There is evidence accumulating to suggest that non-B DNA structures have a potential for genomic instability that induces genomic rearrangements including translocations and deletions. One of the best studied examples is the recurrent t(11;22) constitutional translocation in humans that is mediated by palindromic AT-rich repeats (PATRRs) on chromosomes 11q23 and 22q11. Cloned breakpoint sequences favor adopting a cruciform configuration in vitro. Analysis of the junction fragments implicates frequent double-strand-breaks at the center of both palindromic regions, followed by repair through the nonhomologous end joining pathway. De novo examples of the translocation are detected at a substantial frequency in sperm samples from normal healthy males, but not in other normal somatic tissues or cell lines derived from humans. Further our recent findings indicate that polymorphism of the PATRR affects the frequency of de novo translocation events and symmetrical alleles preferentially generate the translocation. We propose that the symmetric PATRR is likely to adopt a cruciform structure in male meiotic cells, creating genomic instability that leads to the recurrent translocation.